Chr19 Summary



# of exons in each CC

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   1.000   1.000   1.000   2.151   1.000  86.000



# of CC total: 11556
# of CC w/ one exon: 9997



# of CCs by # of exons



mean exon expr. by # of exons



median exon expr. by # of exons





Single exon CCs

## [1] TRUE



location on chr19



median vs. MAD expr. of single exon CCs



There were 400 unique UCSC genes that overlapped with 946 unique CCs. Total number of overlaps was 964.



We now add UCSC KnownGenes to above tracks plots. Note that these are not real transcripts, just the ‘union’ transcripts for each gene constructed by joining all reported isoforms. (note: need to specify fixed() <- TRUE for ucsc track since plot includes ideogram.)



Next, we focus on SPTBN4 which overlapped with 16 single exon CCs.

## 
## uc002onx.3 uc002ony.3 uc002onz.3 uc002ooa.3 uc010egx.3 uc010egy.1 
##         11         16         16          1          9          1 
## uc031rks.1 
##          5





Two exon CCs



# of exons in each CC

## exon_cnts
##    1    2    3    4    5    6 
## 9997  381  117   97   88   96



# of exons/junctions in each CC

## ej_cnts
##    1    2    3    4    5    6 
## 9997  253  151   11   79   16



some CCs with 2 exons but no junctions

##  [1] "gene10021" "gene10052" "gene10061" "gene10084" "gene10146"
##  [6] "gene10276" "gene103"   "gene10358" "gene1038"  "gene10492"
##            gIdx   gStart    gStop kind    start     stop
## 34760 gene10021 54007583 54007739    e 54007583 54007677
## 34761 gene10021 54007583 54007739    e 54007678 54007739




KLK12 region





CC gene models



compare UCSC KLK12 models vs. CCs in region



include nearby genes (KLK9, KLK10, KLK11, KLK12, KLK13)



most likely connected component was gene9317





Plotting exon expression (one CC)



equal width exons



adding annotations





PCA exon expression (one CC)



looking at clustering along the exons at KLK12



exon PCA decomposition (scores)



exon PCA decomposition (loadings)



look at clusters



scores by clusters



expression by clusters





Plotting junction coverage (one CC)



look at clusters



scores by clusters



expression by clusters





Graph-based view (one CC)





R Environment

Running Time

##    user  system elapsed 
##  62.634   2.911  67.470

Last Updated

## [1] "2014-11-04 15:51:58 EST"

Session Information

## R version 3.1.1 (2014-07-10)
## Platform: x86_64-apple-darwin13.3.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] grid      parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] mvnmle_0.1-11                           
##  [2] igraph_0.7.1                            
##  [3] PTAk_1.2-9                              
##  [4] tensor_1.5                              
##  [5] org.Hs.eg.db_2.14.0                     
##  [6] RSQLite_1.0.0                           
##  [7] DBI_0.3.1                               
##  [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
##  [9] BSgenome.Hsapiens.UCSC.hg19_1.3.1000    
## [10] annotate_1.42.1                         
## [11] SplicingGraphs_1.4.1                    
## [12] Rgraphviz_2.8.1                         
## [13] graph_1.42.0                            
## [14] GenomicAlignments_1.0.6                 
## [15] BSgenome_1.32.0                         
## [16] Rsamtools_1.16.1                        
## [17] Biostrings_2.32.1                       
## [18] XVector_0.4.0                           
## [19] GenomicFeatures_1.16.3                  
## [20] AnnotationDbi_1.26.1                    
## [21] Biobase_2.24.0                          
## [22] GenomicRanges_1.16.4                    
## [23] GenomeInfoDb_1.0.2                      
## [24] IRanges_1.22.10                         
## [25] RColorBrewer_1.0-5                      
## [26] ggbio_1.12.10                           
## [27] BiocGenerics_0.10.0                     
## [28] ggplot2_1.0.0                           
## 
## loaded via a namespace (and not attached):
##  [1] acepack_1.3-3.3          base64enc_0.1-2         
##  [3] BatchJobs_1.5            BBmisc_1.8              
##  [5] BiocParallel_0.6.1       biomaRt_2.20.0          
##  [7] biovizBase_1.12.3        bitops_1.0-6            
##  [9] brew_1.0-6               checkmate_1.5.0         
## [11] cluster_1.15.3           codetools_0.2-9         
## [13] colorspace_1.2-4         compiler_3.1.1          
## [15] dichromat_2.0-0          digest_0.6.4            
## [17] evaluate_0.5.5           fail_1.2                
## [19] foreach_1.4.2            foreign_0.8-61          
## [21] formatR_1.0              Formula_1.1-2           
## [23] gridExtra_0.9.1          gtable_0.1.2            
## [25] Hmisc_3.14-5             htmltools_0.2.6         
## [27] iterators_1.0.7          knitr_1.7               
## [29] labeling_0.3             lattice_0.20-29         
## [31] latticeExtra_0.6-26      MASS_7.3-35             
## [33] munsell_0.4.2            nnet_7.3-8              
## [35] plyr_1.8.1               proto_0.3-10            
## [37] Rcpp_0.11.3              RCurl_1.95-4.3          
## [39] reshape2_1.4             rmarkdown_0.3.3         
## [41] rpart_4.1-8              rtracklayer_1.24.2      
## [43] scales_0.2.4             sendmailR_1.2-1         
## [45] splines_3.1.1            stats4_3.1.1            
## [47] stringr_0.6.2            survival_2.37-7         
## [49] tools_3.1.1              VariantAnnotation_1.10.5
## [51] XML_3.98-1.1             xtable_1.7-4            
## [53] yaml_2.1.13              zlibbioc_1.10.0